Starting phenix.real_space_refine on Wed Mar 20 07:19:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w7w_21573/03_2024/6w7w_21573.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w7w_21573/03_2024/6w7w_21573.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w7w_21573/03_2024/6w7w_21573.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w7w_21573/03_2024/6w7w_21573.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w7w_21573/03_2024/6w7w_21573.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w7w_21573/03_2024/6w7w_21573.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.999 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 871 5.49 5 S 33 5.16 5 C 13446 2.51 5 N 5026 2.21 5 O 7507 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 15": "OE1" <-> "OE2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C GLU 160": "OE1" <-> "OE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D GLU 65": "OE1" <-> "OE2" Residue "D ARG 68": "NH1" <-> "NH2" Residue "D ARG 69": "NH1" <-> "NH2" Residue "D ARG 93": "NH1" <-> "NH2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "D GLU 151": "OE1" <-> "OE2" Residue "D ARG 157": "NH1" <-> "NH2" Residue "E PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 16": "OE1" <-> "OE2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 98": "OE1" <-> "OE2" Residue "K ARG 9": "NH1" <-> "NH2" Residue "K ARG 14": "NH1" <-> "NH2" Residue "K ARG 50": "NH1" <-> "NH2" Residue "K TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 70": "OE1" <-> "OE2" Residue "K GLU 76": "OE1" <-> "OE2" Residue "K ARG 83": "NH1" <-> "NH2" Residue "K TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 109": "OD1" <-> "OD2" Residue "N GLU 5": "OE1" <-> "OE2" Residue "N GLU 13": "OE1" <-> "OE2" Residue "N ASP 17": "OD1" <-> "OD2" Residue "N GLU 44": "OE1" <-> "OE2" Residue "O PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 28": "NH1" <-> "NH2" Residue "O ARG 51": "NH1" <-> "NH2" Residue "P ARG 11": "NH1" <-> "NH2" Residue "P ARG 27": "NH1" <-> "NH2" Residue "P GLU 60": "OE1" <-> "OE2" Residue "P ARG 65": "NH1" <-> "NH2" Residue "P ARG 77": "NH1" <-> "NH2" Residue "S PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 59": "OD1" <-> "OD2" Residue "S ARG 60": "NH1" <-> "NH2" Residue "S ARG 74": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26883 Number of models: 1 Model: "" Number of chains: 10 Chain: "2" Number of atoms: 18716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 871, 18716 Classifications: {'RNA': 871} Modifications used: {'rna2p_pur': 68, 'rna2p_pyr': 42, 'rna3p_pur': 438, 'rna3p_pyr': 323} Link IDs: {'rna2p': 110, 'rna3p': 760} Chain breaks: 2 Chain: "C" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1626 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 198} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1145 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 150} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 969 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 123} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 114} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 716 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "O" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "P" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "S" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 664 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Time building chain proxies: 13.64, per 1000 atoms: 0.51 Number of scatterers: 26883 At special positions: 0 Unit cell: (143.782, 187.775, 158.804, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 P 871 15.00 O 7507 8.00 N 5026 7.00 C 13446 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.42 Conformation dependent library (CDL) restraints added in 1.4 seconds 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 40.5% alpha, 17.4% beta 298 base pairs and 466 stacking pairs defined. Time for finding SS restraints: 11.79 Creating SS restraints... Processing helix chain 'C' and resid 8 through 16 removed outlier: 3.868A pdb=" N SER C 12 " --> pdb=" O LYS C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 31 Processing helix chain 'C' and resid 49 through 66 Processing helix chain 'C' and resid 68 through 82 Processing helix chain 'C' and resid 86 through 96 Processing helix chain 'C' and resid 97 through 106 Processing helix chain 'C' and resid 110 through 120 Processing helix chain 'C' and resid 152 through 165 removed outlier: 3.839A pdb=" N LYS C 156 " --> pdb=" O GLN C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 205 Processing helix chain 'D' and resid 55 through 68 Processing helix chain 'D' and resid 109 through 117 removed outlier: 3.964A pdb=" N ALA D 113 " --> pdb=" O GLY D 109 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 146 Processing helix chain 'D' and resid 149 through 158 Processing helix chain 'D' and resid 160 through 165 Processing helix chain 'E' and resid 12 through 16 removed outlier: 5.295A pdb=" N GLU E 16 " --> pdb=" O ASP E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 32 removed outlier: 3.501A pdb=" N GLU E 23 " --> pdb=" O PRO E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 80 removed outlier: 3.924A pdb=" N GLU E 75 " --> pdb=" O ILE E 71 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE E 80 " --> pdb=" O THR E 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 21 Processing helix chain 'G' and resid 30 through 42 Processing helix chain 'G' and resid 94 through 99 removed outlier: 3.621A pdb=" N ALA G 97 " --> pdb=" O LYS G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 120 Processing helix chain 'K' and resid 3 through 9 Processing helix chain 'K' and resid 113 through 118 removed outlier: 3.965A pdb=" N TYR K 117 " --> pdb=" O ALA K 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 15 Processing helix chain 'N' and resid 23 through 43 removed outlier: 3.699A pdb=" N ALA N 29 " --> pdb=" O GLU N 25 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY N 40 " --> pdb=" O ASN N 36 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N HIS N 41 " --> pdb=" O HIS N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 51 through 73 removed outlier: 3.597A pdb=" N LEU N 55 " --> pdb=" O SER N 51 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 85 removed outlier: 4.071A pdb=" N TYR N 77 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLU N 82 " --> pdb=" O THR N 78 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ARG N 83 " --> pdb=" O ARG N 79 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU N 84 " --> pdb=" O LEU N 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 53 through 63 Processing helix chain 'O' and resid 68 through 82 removed outlier: 3.517A pdb=" N ALA O 72 " --> pdb=" O SER O 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 42 removed outlier: 3.548A pdb=" N VAL S 35 " --> pdb=" O PHE S 31 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY S 42 " --> pdb=" O ALA S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 64 removed outlier: 3.759A pdb=" N ALA S 47 " --> pdb=" O ASP S 43 " (cutoff:3.500A) Proline residue: S 56 - end of helix Processing helix chain 'S' and resid 68 through 86 removed outlier: 3.616A pdb=" N ALA S 72 " --> pdb=" O HIS S 68 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU S 86 " --> pdb=" O GLN S 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 128 through 129 removed outlier: 3.884A pdb=" N GLY C 180 " --> pdb=" O VAL C 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 12 through 19 removed outlier: 3.889A pdb=" N LYS D 14 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL D 38 " --> pdb=" O LYS D 14 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU D 36 " --> pdb=" O ILE D 16 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL D 18 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR D 34 " --> pdb=" O VAL D 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 22 through 24 removed outlier: 3.707A pdb=" N LYS D 23 " --> pdb=" O ILE D 30 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE D 30 " --> pdb=" O LYS D 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 85 through 88 Processing sheet with id=AA5, first strand: chain 'E' and resid 40 through 45 removed outlier: 5.464A pdb=" N ASP E 41 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU E 61 " --> pdb=" O ASP E 41 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY E 43 " --> pdb=" O TYR E 59 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA E 57 " --> pdb=" O ARG E 45 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS E 58 " --> pdb=" O VAL E 10 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL E 10 " --> pdb=" O HIS E 58 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL E 60 " --> pdb=" O PHE E 8 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE E 8 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLU E 5 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL E 89 " --> pdb=" O GLU E 5 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL E 7 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N SER E 87 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N MET E 9 " --> pdb=" O ILE E 85 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 24 through 28 removed outlier: 4.506A pdb=" N ASP G 48 " --> pdb=" O THR G 62 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 65 through 66 removed outlier: 3.547A pdb=" N PHE G 66 " --> pdb=" O LYS G 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 74 through 77 removed outlier: 3.598A pdb=" N GLN G 76 " --> pdb=" O TYR G 128 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ILE G 125 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N SER G 105 " --> pdb=" O ILE G 125 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS G 127 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL G 104 " --> pdb=" O MET G 111 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET G 111 " --> pdb=" O VAL G 104 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 62 through 66 removed outlier: 3.608A pdb=" N CYS K 53 " --> pdb=" O SER K 65 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ARG K 50 " --> pdb=" O THR K 39 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR K 39 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL K 52 " --> pdb=" O VAL K 37 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N VAL K 37 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ARG K 54 " --> pdb=" O THR K 35 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS K 30 " --> pdb=" O ILE K 82 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE K 82 " --> pdb=" O LYS K 30 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'O' and resid 2 through 8 removed outlier: 3.728A pdb=" N GLU O 34 " --> pdb=" O VAL O 21 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'O' and resid 38 through 39 Processing sheet with id=AB3, first strand: chain 'P' and resid 8 through 14 removed outlier: 8.875A pdb=" N GLN P 9 " --> pdb=" O GLU P 26 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLU P 26 " --> pdb=" O GLN P 9 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL P 22 " --> pdb=" O VAL P 13 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TRP P 73 " --> pdb=" O HIS P 45 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU P 75 " --> pdb=" O HIS P 47 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLU P 60 " --> pdb=" O VAL P 76 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N VAL P 78 " --> pdb=" O VAL P 58 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VAL P 58 " --> pdb=" O VAL P 78 " (cutoff:3.500A) 359 hydrogen bonds defined for protein. 1023 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 754 hydrogen bonds 1214 hydrogen bond angles 0 basepair planarities 298 basepair parallelities 466 stacking parallelities Total time for adding SS restraints: 16.72 Time building geometry restraints manager: 15.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3950 1.33 - 1.45: 12379 1.45 - 1.57: 11112 1.57 - 1.69: 1739 1.69 - 1.81: 58 Bond restraints: 29238 Sorted by residual: bond pdb=" N1 U 2 287 " pdb=" C2 U 2 287 " ideal model delta sigma weight residual 1.381 1.402 -0.021 2.00e-02 2.50e+03 1.11e+00 bond pdb=" C2 C 2 613 " pdb=" O2 C 2 613 " ideal model delta sigma weight residual 1.240 1.220 0.020 2.00e-02 2.50e+03 9.98e-01 bond pdb=" CA ARG C 47 " pdb=" CB ARG C 47 " ideal model delta sigma weight residual 1.524 1.537 -0.012 1.22e-02 6.72e+03 9.92e-01 bond pdb=" C VAL E 18 " pdb=" N PRO E 19 " ideal model delta sigma weight residual 1.335 1.347 -0.012 1.28e-02 6.10e+03 9.21e-01 bond pdb=" N9 G 2 627 " pdb=" C4 G 2 627 " ideal model delta sigma weight residual 1.375 1.393 -0.018 2.00e-02 2.50e+03 7.93e-01 ... (remaining 29233 not shown) Histogram of bond angle deviations from ideal: 99.95 - 106.82: 5323 106.82 - 113.70: 17795 113.70 - 120.57: 11042 120.57 - 127.45: 7841 127.45 - 134.32: 1807 Bond angle restraints: 43808 Sorted by residual: angle pdb=" C GLU N 44 " pdb=" N HIS N 45 " pdb=" CA HIS N 45 " ideal model delta sigma weight residual 121.54 127.57 -6.03 1.91e+00 2.74e-01 9.98e+00 angle pdb=" C2' G 2 628 " pdb=" C1' G 2 628 " pdb=" N9 G 2 628 " ideal model delta sigma weight residual 112.00 116.57 -4.57 1.50e+00 4.44e-01 9.30e+00 angle pdb=" C1' U 2 287 " pdb=" N1 U 2 287 " pdb=" C2 U 2 287 " ideal model delta sigma weight residual 117.70 126.60 -8.90 3.00e+00 1.11e-01 8.79e+00 angle pdb=" C ALA K 101 " pdb=" N LEU K 102 " pdb=" CA LEU K 102 " ideal model delta sigma weight residual 121.54 127.15 -5.61 1.91e+00 2.74e-01 8.63e+00 angle pdb=" N VAL O 36 " pdb=" CA VAL O 36 " pdb=" C VAL O 36 " ideal model delta sigma weight residual 111.62 109.37 2.25 7.90e-01 1.60e+00 8.14e+00 ... (remaining 43803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 16323 35.40 - 70.79: 2167 70.79 - 106.19: 249 106.19 - 141.58: 5 141.58 - 176.97: 6 Dihedral angle restraints: 18750 sinusoidal: 15746 harmonic: 3004 Sorted by residual: dihedral pdb=" O4' U 2 439 " pdb=" C1' U 2 439 " pdb=" N1 U 2 439 " pdb=" C2 U 2 439 " ideal model delta sinusoidal sigma weight residual 200.00 40.35 159.65 1 1.50e+01 4.44e-03 8.27e+01 dihedral pdb=" O4' U 2 4 " pdb=" C1' U 2 4 " pdb=" N1 U 2 4 " pdb=" C2 U 2 4 " ideal model delta sinusoidal sigma weight residual 200.00 45.13 154.87 1 1.50e+01 4.44e-03 8.13e+01 dihedral pdb=" O4' U 2 365 " pdb=" C1' U 2 365 " pdb=" N1 U 2 365 " pdb=" C2 U 2 365 " ideal model delta sinusoidal sigma weight residual 200.00 62.24 137.76 1 1.50e+01 4.44e-03 7.43e+01 ... (remaining 18747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 5302 0.060 - 0.120: 279 0.120 - 0.179: 19 0.179 - 0.239: 4 0.239 - 0.299: 2 Chirality restraints: 5606 Sorted by residual: chirality pdb=" CB ILE D 106 " pdb=" CA ILE D 106 " pdb=" CG1 ILE D 106 " pdb=" CG2 ILE D 106 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C1' G 2 628 " pdb=" O4' G 2 628 " pdb=" C2' G 2 628 " pdb=" N9 G 2 628 " both_signs ideal model delta sigma weight residual False 2.46 2.16 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C1' C 2 754 " pdb=" O4' C 2 754 " pdb=" C2' C 2 754 " pdb=" N1 C 2 754 " both_signs ideal model delta sigma weight residual False 2.47 2.26 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 5603 not shown) Planarity restraints: 2307 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C 2 613 " -0.010 2.00e-02 2.50e+03 2.05e-02 9.42e+00 pdb=" N1 C 2 613 " -0.001 2.00e-02 2.50e+03 pdb=" C2 C 2 613 " 0.051 2.00e-02 2.50e+03 pdb=" O2 C 2 613 " -0.026 2.00e-02 2.50e+03 pdb=" N3 C 2 613 " -0.006 2.00e-02 2.50e+03 pdb=" C4 C 2 613 " 0.011 2.00e-02 2.50e+03 pdb=" N4 C 2 613 " -0.013 2.00e-02 2.50e+03 pdb=" C5 C 2 613 " -0.005 2.00e-02 2.50e+03 pdb=" C6 C 2 613 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 2 628 " 0.035 2.00e-02 2.50e+03 1.48e-02 6.58e+00 pdb=" N9 G 2 628 " -0.032 2.00e-02 2.50e+03 pdb=" C8 G 2 628 " -0.012 2.00e-02 2.50e+03 pdb=" N7 G 2 628 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G 2 628 " 0.006 2.00e-02 2.50e+03 pdb=" C6 G 2 628 " 0.006 2.00e-02 2.50e+03 pdb=" O6 G 2 628 " 0.009 2.00e-02 2.50e+03 pdb=" N1 G 2 628 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G 2 628 " -0.006 2.00e-02 2.50e+03 pdb=" N2 G 2 628 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G 2 628 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G 2 628 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 2 629 " 0.030 2.00e-02 2.50e+03 1.44e-02 5.71e+00 pdb=" N9 A 2 629 " -0.035 2.00e-02 2.50e+03 pdb=" C8 A 2 629 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A 2 629 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A 2 629 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A 2 629 " 0.006 2.00e-02 2.50e+03 pdb=" N6 A 2 629 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A 2 629 " 0.000 2.00e-02 2.50e+03 pdb=" C2 A 2 629 " -0.006 2.00e-02 2.50e+03 pdb=" N3 A 2 629 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A 2 629 " -0.001 2.00e-02 2.50e+03 ... (remaining 2304 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 1957 2.70 - 3.25: 25511 3.25 - 3.80: 54890 3.80 - 4.35: 67062 4.35 - 4.90: 89200 Nonbonded interactions: 238620 Sorted by model distance: nonbonded pdb=" O2 U 2 49 " pdb=" N2 G 2 361 " model vdw 2.156 2.520 nonbonded pdb=" OP2 G 2 82 " pdb=" N2 G 2 82 " model vdw 2.162 2.520 nonbonded pdb=" O4 U 2 652 " pdb=" O2' G 2 752 " model vdw 2.195 2.440 nonbonded pdb=" O2 U 2 835 " pdb=" O6 G 2 851 " model vdw 2.213 2.432 nonbonded pdb=" O2' C 2 136 " pdb=" O GLY O 64 " model vdw 2.228 2.440 ... (remaining 238615 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.160 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 83.350 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 29238 Z= 0.114 Angle : 0.495 8.896 43808 Z= 0.265 Chirality : 0.029 0.299 5606 Planarity : 0.003 0.054 2307 Dihedral : 23.619 176.975 16810 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.12 % Allowed : 3.29 % Favored : 96.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.23), residues: 1029 helix: -0.94 (0.23), residues: 378 sheet: -2.67 (0.35), residues: 166 loop : -2.29 (0.25), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP O 60 HIS 0.006 0.001 HIS E 3 PHE 0.005 0.001 PHE P 28 TYR 0.005 0.001 TYR E 4 ARG 0.002 0.000 ARG C 47 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 272 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 GLN cc_start: 0.8947 (mt0) cc_final: 0.8742 (mt0) REVERT: C 93 LEU cc_start: 0.9195 (mp) cc_final: 0.8717 (tp) REVERT: C 124 MET cc_start: 0.8030 (mtp) cc_final: 0.7698 (mtm) REVERT: D 20 ARG cc_start: 0.7837 (ttt-90) cc_final: 0.7402 (ttm-80) REVERT: D 64 MET cc_start: 0.8918 (tmm) cc_final: 0.8689 (tmm) REVERT: D 66 LYS cc_start: 0.7822 (ttmt) cc_final: 0.7347 (tmtt) REVERT: D 71 MET cc_start: 0.7390 (mmp) cc_final: 0.5913 (mmp) REVERT: D 82 GLN cc_start: 0.7433 (mm-40) cc_final: 0.6615 (mm-40) REVERT: D 95 PHE cc_start: 0.8898 (t80) cc_final: 0.8687 (t80) REVERT: D 132 ASN cc_start: 0.7613 (t0) cc_final: 0.7397 (t0) REVERT: G 125 ILE cc_start: 0.8879 (mt) cc_final: 0.8629 (mt) REVERT: N 14 PHE cc_start: 0.8525 (m-80) cc_final: 0.7748 (m-80) REVERT: N 58 MET cc_start: 0.6012 (ptt) cc_final: 0.5785 (tmm) REVERT: O 25 ARG cc_start: 0.9230 (mtm110) cc_final: 0.8952 (ptp90) REVERT: O 63 GLN cc_start: 0.8751 (mm110) cc_final: 0.8226 (mm-40) REVERT: O 80 LYS cc_start: 0.9399 (tmmt) cc_final: 0.8831 (ptpt) REVERT: P 11 ARG cc_start: 0.8286 (mtp85) cc_final: 0.7956 (ttm-80) REVERT: P 81 LYS cc_start: 0.9039 (ttpp) cc_final: 0.8777 (tptp) REVERT: S 32 ILE cc_start: 0.9205 (pt) cc_final: 0.8983 (pt) outliers start: 1 outliers final: 0 residues processed: 273 average time/residue: 0.4223 time to fit residues: 172.2907 Evaluate side-chains 200 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 79 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 20.0000 chunk 147 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 109 optimal weight: 30.0000 chunk 170 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN E 52 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 26 ASN O 79 ASN ** P 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 29238 Z= 0.282 Angle : 0.632 9.418 43808 Z= 0.317 Chirality : 0.034 0.303 5606 Planarity : 0.005 0.089 2307 Dihedral : 24.206 175.327 14772 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.70 % Allowed : 17.96 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.25), residues: 1029 helix: 0.01 (0.25), residues: 386 sheet: -2.03 (0.39), residues: 172 loop : -1.84 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 73 HIS 0.008 0.002 HIS E 3 PHE 0.040 0.003 PHE N 42 TYR 0.013 0.002 TYR E 49 ARG 0.008 0.001 ARG N 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 212 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 202 GLU cc_start: 0.8747 (pt0) cc_final: 0.8159 (tp30) REVERT: D 20 ARG cc_start: 0.7752 (ttt-90) cc_final: 0.7527 (ttm-80) REVERT: D 82 GLN cc_start: 0.7509 (mm-40) cc_final: 0.6650 (mm-40) REVERT: D 97 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8560 (pt0) REVERT: D 132 ASN cc_start: 0.7879 (t0) cc_final: 0.7587 (t0) REVERT: G 12 THR cc_start: 0.9351 (p) cc_final: 0.9113 (t) REVERT: G 36 ILE cc_start: 0.9484 (OUTLIER) cc_final: 0.9252 (tt) REVERT: G 91 GLU cc_start: 0.8711 (tt0) cc_final: 0.8495 (tt0) REVERT: K 14 ARG cc_start: 0.7980 (mmm-85) cc_final: 0.7653 (mmm160) REVERT: K 75 GLN cc_start: 0.8457 (pp30) cc_final: 0.8221 (pp30) REVERT: N 31 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8725 (mm) REVERT: N 62 ARG cc_start: 0.8486 (ttp-110) cc_final: 0.8282 (ttm-80) REVERT: O 25 ARG cc_start: 0.9281 (mtm110) cc_final: 0.9043 (ptp90) REVERT: O 63 GLN cc_start: 0.9148 (mm110) cc_final: 0.8495 (mm-40) REVERT: O 80 LYS cc_start: 0.9445 (tmmt) cc_final: 0.8932 (pttm) REVERT: P 11 ARG cc_start: 0.8152 (mtp85) cc_final: 0.7795 (ttm-80) outliers start: 23 outliers final: 16 residues processed: 223 average time/residue: 0.4192 time to fit residues: 142.3929 Evaluate side-chains 210 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 191 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 28 PHE Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain S residue 3 ASN Chi-restraints excluded: chain S residue 59 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 171 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 chunk 152 optimal weight: 9.9990 chunk 169 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 137 optimal weight: 0.0030 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 GLN O 63 GLN ** P 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 29238 Z= 0.182 Angle : 0.564 12.577 43808 Z= 0.283 Chirality : 0.032 0.291 5606 Planarity : 0.004 0.044 2307 Dihedral : 24.110 176.665 14772 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.40 % Allowed : 20.42 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.26), residues: 1029 helix: 0.43 (0.26), residues: 381 sheet: -1.98 (0.39), residues: 166 loop : -1.60 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 73 HIS 0.005 0.001 HIS S 68 PHE 0.031 0.002 PHE N 42 TYR 0.009 0.001 TYR E 49 ARG 0.007 0.000 ARG C 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 215 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 47 ARG cc_start: 0.8754 (ttp80) cc_final: 0.8478 (ttp80) REVERT: C 124 MET cc_start: 0.7612 (mtp) cc_final: 0.7005 (mtm) REVERT: C 202 GLU cc_start: 0.8725 (pt0) cc_final: 0.8194 (tp30) REVERT: D 82 GLN cc_start: 0.7342 (mm-40) cc_final: 0.7023 (mm-40) REVERT: D 88 VAL cc_start: 0.8664 (OUTLIER) cc_final: 0.8335 (m) REVERT: D 132 ASN cc_start: 0.7770 (t0) cc_final: 0.7410 (t0) REVERT: E 9 MET cc_start: 0.7881 (pmm) cc_final: 0.7207 (ppp) REVERT: E 90 MET cc_start: 0.7950 (mmm) cc_final: 0.6471 (ttm) REVERT: G 27 MET cc_start: 0.8647 (ptp) cc_final: 0.8355 (ptp) REVERT: G 54 ASP cc_start: 0.8350 (p0) cc_final: 0.8149 (p0) REVERT: G 59 LEU cc_start: 0.9297 (tp) cc_final: 0.8809 (tp) REVERT: G 63 LEU cc_start: 0.9073 (mp) cc_final: 0.8845 (mp) REVERT: K 5 ASN cc_start: 0.8502 (t0) cc_final: 0.8031 (t0) REVERT: K 14 ARG cc_start: 0.7949 (mmm-85) cc_final: 0.7609 (mmm160) REVERT: K 75 GLN cc_start: 0.8463 (pp30) cc_final: 0.8206 (pp30) REVERT: O 25 ARG cc_start: 0.9233 (mtm110) cc_final: 0.9006 (ptp90) REVERT: O 63 GLN cc_start: 0.9132 (mm-40) cc_final: 0.8783 (mm-40) REVERT: O 80 LYS cc_start: 0.9455 (tmmt) cc_final: 0.8886 (ptpt) REVERT: P 11 ARG cc_start: 0.8051 (mtp85) cc_final: 0.7778 (ttm-80) REVERT: P 21 ILE cc_start: 0.9654 (pt) cc_final: 0.9438 (mt) outliers start: 29 outliers final: 19 residues processed: 230 average time/residue: 0.4176 time to fit residues: 148.0929 Evaluate side-chains 216 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 196 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain P residue 28 PHE Chi-restraints excluded: chain P residue 57 ASP Chi-restraints excluded: chain P residue 63 GLU Chi-restraints excluded: chain S residue 3 ASN Chi-restraints excluded: chain S residue 40 GLU Chi-restraints excluded: chain S residue 59 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 0.0570 chunk 128 optimal weight: 40.0000 chunk 88 optimal weight: 0.0670 chunk 18 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 chunk 171 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 162 optimal weight: 30.0000 chunk 48 optimal weight: 10.0000 overall best weight: 1.4040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN E 3 HIS E 52 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 GLN S 55 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 29238 Z= 0.131 Angle : 0.535 11.299 43808 Z= 0.269 Chirality : 0.031 0.288 5606 Planarity : 0.004 0.070 2307 Dihedral : 23.985 176.766 14772 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.29 % Allowed : 22.30 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.26), residues: 1029 helix: 0.63 (0.26), residues: 381 sheet: -1.76 (0.39), residues: 160 loop : -1.45 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 73 HIS 0.015 0.001 HIS E 3 PHE 0.024 0.001 PHE N 42 TYR 0.018 0.001 TYR C 76 ARG 0.009 0.000 ARG D 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 211 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 MET cc_start: 0.7573 (mtp) cc_final: 0.6997 (mtm) REVERT: C 202 GLU cc_start: 0.8611 (pt0) cc_final: 0.8130 (tp30) REVERT: D 88 VAL cc_start: 0.8670 (OUTLIER) cc_final: 0.8337 (m) REVERT: D 132 ASN cc_start: 0.7581 (t0) cc_final: 0.7276 (t0) REVERT: E 73 GLU cc_start: 0.9269 (tm-30) cc_final: 0.8874 (mt-10) REVERT: E 90 MET cc_start: 0.7915 (mmm) cc_final: 0.6712 (mtt) REVERT: G 54 ASP cc_start: 0.8222 (p0) cc_final: 0.7911 (p0) REVERT: K 5 ASN cc_start: 0.8509 (t0) cc_final: 0.8018 (t0) REVERT: K 14 ARG cc_start: 0.7932 (mmm-85) cc_final: 0.7573 (mmm160) REVERT: K 20 ASN cc_start: 0.9113 (p0) cc_final: 0.8847 (p0) REVERT: K 75 GLN cc_start: 0.8531 (pp30) cc_final: 0.8271 (pp30) REVERT: N 25 GLU cc_start: 0.9414 (mp0) cc_final: 0.9057 (pm20) REVERT: O 25 ARG cc_start: 0.9176 (mtm110) cc_final: 0.8954 (ptp90) REVERT: O 63 GLN cc_start: 0.9046 (mm-40) cc_final: 0.8765 (mm-40) REVERT: O 80 LYS cc_start: 0.9484 (tmmt) cc_final: 0.8915 (ptpt) REVERT: P 21 ILE cc_start: 0.9651 (pt) cc_final: 0.9199 (mm) outliers start: 28 outliers final: 20 residues processed: 231 average time/residue: 0.4074 time to fit residues: 145.5750 Evaluate side-chains 213 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 192 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 98 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain P residue 28 PHE Chi-restraints excluded: chain P residue 57 ASP Chi-restraints excluded: chain P residue 63 GLU Chi-restraints excluded: chain S residue 3 ASN Chi-restraints excluded: chain S residue 40 GLU Chi-restraints excluded: chain S residue 57 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 0.3980 chunk 103 optimal weight: 40.0000 chunk 2 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 155 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 163 optimal weight: 0.3980 chunk 45 optimal weight: 10.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 GLN S 52 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 29238 Z= 0.317 Angle : 0.665 11.252 43808 Z= 0.333 Chirality : 0.036 0.290 5606 Planarity : 0.005 0.049 2307 Dihedral : 24.105 173.290 14772 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 4.58 % Allowed : 23.12 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.25), residues: 1029 helix: 0.39 (0.25), residues: 384 sheet: -1.78 (0.38), residues: 167 loop : -1.44 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP P 73 HIS 0.019 0.002 HIS C 41 PHE 0.019 0.002 PHE N 42 TYR 0.013 0.002 TYR G 128 ARG 0.006 0.001 ARG P 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 196 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 GLN cc_start: 0.8411 (mm-40) cc_final: 0.7984 (mm-40) REVERT: C 124 MET cc_start: 0.7862 (mtp) cc_final: 0.7447 (mtm) REVERT: C 202 GLU cc_start: 0.8737 (pt0) cc_final: 0.8343 (tp30) REVERT: D 14 LYS cc_start: 0.9017 (ptpp) cc_final: 0.8651 (ptpp) REVERT: D 61 GLN cc_start: 0.8964 (pp30) cc_final: 0.8324 (tp-100) REVERT: D 64 MET cc_start: 0.9107 (ppp) cc_final: 0.8464 (ppp) REVERT: D 82 GLN cc_start: 0.7324 (mm-40) cc_final: 0.7119 (mm-40) REVERT: E 9 MET cc_start: 0.8150 (pmm) cc_final: 0.7399 (ppp) REVERT: E 90 MET cc_start: 0.7881 (mmm) cc_final: 0.6437 (ttm) REVERT: G 54 ASP cc_start: 0.8511 (p0) cc_final: 0.8220 (p0) REVERT: K 5 ASN cc_start: 0.8632 (t0) cc_final: 0.8162 (t0) REVERT: K 75 GLN cc_start: 0.8638 (pp30) cc_final: 0.8380 (pp30) REVERT: N 25 GLU cc_start: 0.9414 (mp0) cc_final: 0.9072 (pm20) REVERT: N 31 LEU cc_start: 0.8958 (mp) cc_final: 0.8187 (tp) REVERT: O 25 ARG cc_start: 0.9296 (mtm110) cc_final: 0.8988 (ptp90) REVERT: O 63 GLN cc_start: 0.9253 (mm-40) cc_final: 0.8646 (mm-40) REVERT: O 80 LYS cc_start: 0.9460 (tmmt) cc_final: 0.8891 (ptpt) outliers start: 39 outliers final: 34 residues processed: 222 average time/residue: 0.4026 time to fit residues: 137.9337 Evaluate side-chains 218 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 184 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 21 MET Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 98 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 57 ASP Chi-restraints excluded: chain P residue 63 GLU Chi-restraints excluded: chain S residue 3 ASN Chi-restraints excluded: chain S residue 40 GLU Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 59 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 10.0000 chunk 163 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 chunk 150 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 HIS N 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 29238 Z= 0.392 Angle : 0.752 11.076 43808 Z= 0.377 Chirality : 0.040 0.269 5606 Planarity : 0.005 0.045 2307 Dihedral : 24.363 171.883 14772 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 24.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 6.22 % Allowed : 23.59 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.25), residues: 1029 helix: 0.21 (0.25), residues: 391 sheet: -1.82 (0.37), residues: 170 loop : -1.62 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP P 73 HIS 0.011 0.002 HIS C 41 PHE 0.016 0.002 PHE E 80 TYR 0.018 0.002 TYR E 49 ARG 0.006 0.001 ARG E 2 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 193 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 GLN cc_start: 0.7674 (tp40) cc_final: 0.7370 (tp40) REVERT: C 202 GLU cc_start: 0.8796 (pt0) cc_final: 0.8484 (tp30) REVERT: D 14 LYS cc_start: 0.8973 (ptpp) cc_final: 0.8666 (ptpp) REVERT: D 61 GLN cc_start: 0.8975 (pp30) cc_final: 0.8374 (tp-100) REVERT: D 64 MET cc_start: 0.9102 (ppp) cc_final: 0.8487 (ppp) REVERT: D 66 LYS cc_start: 0.8142 (ttmt) cc_final: 0.7594 (tttt) REVERT: D 88 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8257 (m) REVERT: E 9 MET cc_start: 0.8166 (pmm) cc_final: 0.7484 (ppp) REVERT: E 49 TYR cc_start: -0.0762 (OUTLIER) cc_final: -0.1114 (m-80) REVERT: E 90 MET cc_start: 0.7843 (mmm) cc_final: 0.6497 (ttm) REVERT: G 54 ASP cc_start: 0.8474 (p0) cc_final: 0.8161 (p0) REVERT: K 5 ASN cc_start: 0.8572 (t0) cc_final: 0.8081 (t0) REVERT: K 75 GLN cc_start: 0.8699 (pp30) cc_final: 0.8484 (pp30) REVERT: N 65 LEU cc_start: 0.8537 (tp) cc_final: 0.8221 (pp) REVERT: O 25 ARG cc_start: 0.9318 (mtm110) cc_final: 0.9096 (ptp90) REVERT: O 63 GLN cc_start: 0.9345 (mm-40) cc_final: 0.8609 (mm-40) REVERT: O 80 LYS cc_start: 0.9416 (tmmt) cc_final: 0.8863 (ptpt) REVERT: P 39 LYS cc_start: 0.9381 (tttt) cc_final: 0.9022 (tttm) REVERT: P 67 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8644 (mm) REVERT: S 36 TYR cc_start: 0.8971 (OUTLIER) cc_final: 0.8504 (t80) outliers start: 53 outliers final: 41 residues processed: 228 average time/residue: 0.3907 time to fit residues: 138.9549 Evaluate side-chains 227 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 182 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 21 MET Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 98 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 48 ASP Chi-restraints excluded: chain P residue 57 ASP Chi-restraints excluded: chain P residue 63 GLU Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 80 GLU Chi-restraints excluded: chain S residue 3 ASN Chi-restraints excluded: chain S residue 36 TYR Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 59 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 113 optimal weight: 30.0000 chunk 110 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 29238 Z= 0.203 Angle : 0.619 11.167 43808 Z= 0.310 Chirality : 0.035 0.295 5606 Planarity : 0.004 0.045 2307 Dihedral : 24.181 174.280 14772 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.81 % Allowed : 26.41 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.26), residues: 1029 helix: 0.43 (0.26), residues: 394 sheet: -1.67 (0.38), residues: 175 loop : -1.36 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP P 73 HIS 0.008 0.001 HIS N 45 PHE 0.031 0.002 PHE D 95 TYR 0.016 0.002 TYR G 128 ARG 0.008 0.000 ARG G 117 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 196 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 GLN cc_start: 0.7537 (tp40) cc_final: 0.7272 (tp40) REVERT: C 202 GLU cc_start: 0.8670 (pt0) cc_final: 0.8378 (tp30) REVERT: D 14 LYS cc_start: 0.8955 (ptpp) cc_final: 0.8596 (ptpp) REVERT: D 61 GLN cc_start: 0.8946 (pp30) cc_final: 0.8388 (tp-100) REVERT: D 64 MET cc_start: 0.9098 (ppp) cc_final: 0.8534 (ppp) REVERT: D 66 LYS cc_start: 0.8100 (ttmt) cc_final: 0.7565 (tttt) REVERT: D 88 VAL cc_start: 0.8716 (OUTLIER) cc_final: 0.8380 (m) REVERT: D 156 LYS cc_start: 0.9495 (ptpt) cc_final: 0.9219 (ptpp) REVERT: E 9 MET cc_start: 0.8115 (pmm) cc_final: 0.7429 (ppp) REVERT: E 90 MET cc_start: 0.7853 (mmm) cc_final: 0.7033 (ttm) REVERT: E 91 ARG cc_start: 0.7155 (mtp180) cc_final: 0.6616 (mtm-85) REVERT: G 54 ASP cc_start: 0.8510 (p0) cc_final: 0.8197 (p0) REVERT: K 5 ASN cc_start: 0.8538 (t0) cc_final: 0.8308 (t0) REVERT: K 75 GLN cc_start: 0.8660 (pp30) cc_final: 0.8411 (pp30) REVERT: N 25 GLU cc_start: 0.9322 (mp0) cc_final: 0.8990 (pm20) REVERT: O 63 GLN cc_start: 0.9272 (mm-40) cc_final: 0.8734 (mm-40) REVERT: O 80 LYS cc_start: 0.9418 (tmmt) cc_final: 0.8855 (ptpt) outliers start: 41 outliers final: 33 residues processed: 223 average time/residue: 0.3985 time to fit residues: 137.2181 Evaluate side-chains 220 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 186 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 21 MET Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 27 CYS Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 98 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain P residue 57 ASP Chi-restraints excluded: chain S residue 3 ASN Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 59 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 108 optimal weight: 0.1980 chunk 54 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 123 optimal weight: 20.0000 chunk 89 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 142 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 GLN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 GLN ** S 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29238 Z= 0.151 Angle : 0.581 11.511 43808 Z= 0.290 Chirality : 0.032 0.290 5606 Planarity : 0.004 0.048 2307 Dihedral : 24.025 175.741 14772 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.34 % Allowed : 28.17 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.26), residues: 1029 helix: 0.68 (0.26), residues: 383 sheet: -1.61 (0.38), residues: 164 loop : -1.16 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP P 73 HIS 0.006 0.001 HIS N 45 PHE 0.014 0.001 PHE E 80 TYR 0.023 0.001 TYR N 68 ARG 0.009 0.001 ARG P 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 202 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 GLN cc_start: 0.7749 (tp40) cc_final: 0.7516 (tp40) REVERT: D 14 LYS cc_start: 0.8940 (ptpp) cc_final: 0.8586 (ptpp) REVERT: D 88 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8364 (m) REVERT: D 135 ASN cc_start: 0.8724 (m-40) cc_final: 0.8501 (m-40) REVERT: E 9 MET cc_start: 0.8175 (pmm) cc_final: 0.7545 (ppp) REVERT: E 75 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7270 (pm20) REVERT: E 90 MET cc_start: 0.7889 (mmm) cc_final: 0.6873 (ttm) REVERT: E 91 ARG cc_start: 0.7034 (mtp180) cc_final: 0.6602 (mtm-85) REVERT: G 54 ASP cc_start: 0.8382 (p0) cc_final: 0.8128 (p0) REVERT: K 5 ASN cc_start: 0.8524 (t0) cc_final: 0.8296 (t0) REVERT: K 75 GLN cc_start: 0.8678 (pp30) cc_final: 0.8477 (pp30) REVERT: N 25 GLU cc_start: 0.9399 (mp0) cc_final: 0.9013 (pm20) REVERT: O 80 LYS cc_start: 0.9441 (tmmt) cc_final: 0.8870 (ptpt) REVERT: P 21 ILE cc_start: 0.9622 (pt) cc_final: 0.9358 (mt) REVERT: P 26 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7964 (tm-30) REVERT: P 39 LYS cc_start: 0.9395 (tttt) cc_final: 0.9141 (tptm) REVERT: P 67 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8629 (mm) REVERT: S 36 TYR cc_start: 0.8889 (OUTLIER) cc_final: 0.8435 (t80) outliers start: 37 outliers final: 30 residues processed: 228 average time/residue: 0.4066 time to fit residues: 143.7412 Evaluate side-chains 223 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 189 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 21 MET Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 27 CYS Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 98 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 57 ASP Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain S residue 3 ASN Chi-restraints excluded: chain S residue 36 TYR Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 59 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 8.9990 chunk 158 optimal weight: 8.9990 chunk 168 optimal weight: 0.0020 chunk 101 optimal weight: 6.9990 chunk 73 optimal weight: 20.0000 chunk 132 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 178 optimal weight: 8.9990 overall best weight: 5.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 GLN O 63 GLN P 45 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 29238 Z= 0.308 Angle : 0.682 15.986 43808 Z= 0.338 Chirality : 0.035 0.297 5606 Planarity : 0.005 0.063 2307 Dihedral : 24.047 173.482 14772 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 21.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 4.81 % Allowed : 28.76 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.26), residues: 1029 helix: 0.55 (0.26), residues: 384 sheet: -1.66 (0.36), residues: 188 loop : -1.25 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 73 HIS 0.006 0.001 HIS O 9 PHE 0.035 0.002 PHE D 95 TYR 0.017 0.002 TYR N 68 ARG 0.009 0.001 ARG G 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 190 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 GLN cc_start: 0.7779 (tp40) cc_final: 0.7514 (tp40) REVERT: D 14 LYS cc_start: 0.8933 (ptpp) cc_final: 0.8558 (ptpp) REVERT: D 61 GLN cc_start: 0.8971 (pp30) cc_final: 0.8507 (tp-100) REVERT: D 88 VAL cc_start: 0.8686 (OUTLIER) cc_final: 0.8364 (t) REVERT: E 9 MET cc_start: 0.8207 (pmm) cc_final: 0.7542 (ppp) REVERT: E 75 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7336 (pm20) REVERT: E 90 MET cc_start: 0.7886 (mmm) cc_final: 0.7593 (mtt) REVERT: E 91 ARG cc_start: 0.7086 (mtp180) cc_final: 0.6452 (mtm-85) REVERT: G 54 ASP cc_start: 0.8402 (p0) cc_final: 0.8094 (p0) REVERT: K 5 ASN cc_start: 0.8621 (t0) cc_final: 0.8124 (t0) REVERT: K 75 GLN cc_start: 0.8673 (pp30) cc_final: 0.8405 (pp30) REVERT: N 25 GLU cc_start: 0.9402 (mp0) cc_final: 0.9041 (pm20) REVERT: N 58 MET cc_start: 0.5165 (ppp) cc_final: 0.4738 (ppp) REVERT: O 55 ASP cc_start: 0.8564 (p0) cc_final: 0.8281 (p0) REVERT: O 80 LYS cc_start: 0.9445 (tmmt) cc_final: 0.8890 (ptpt) REVERT: P 67 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8585 (mm) REVERT: S 36 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.8458 (t80) outliers start: 41 outliers final: 34 residues processed: 219 average time/residue: 0.3950 time to fit residues: 134.1035 Evaluate side-chains 220 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 182 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 21 MET Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 27 CYS Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 98 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 63 GLN Chi-restraints excluded: chain P residue 28 PHE Chi-restraints excluded: chain P residue 57 ASP Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain S residue 3 ASN Chi-restraints excluded: chain S residue 36 TYR Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 59 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 187 optimal weight: 9.9990 chunk 172 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 115 optimal weight: 0.9990 chunk 91 optimal weight: 20.0000 chunk 118 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 29238 Z= 0.337 Angle : 0.706 11.210 43808 Z= 0.354 Chirality : 0.038 0.301 5606 Planarity : 0.005 0.047 2307 Dihedral : 24.193 172.464 14772 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 23.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 4.58 % Allowed : 28.99 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.26), residues: 1029 helix: 0.41 (0.26), residues: 393 sheet: -1.81 (0.36), residues: 186 loop : -1.35 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP P 73 HIS 0.006 0.001 HIS N 45 PHE 0.018 0.002 PHE E 80 TYR 0.025 0.002 TYR C 51 ARG 0.009 0.001 ARG G 117 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 190 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 GLN cc_start: 0.7840 (tp40) cc_final: 0.7594 (tp40) REVERT: D 14 LYS cc_start: 0.8957 (ptpp) cc_final: 0.8635 (ptpp) REVERT: D 22 SER cc_start: 0.8369 (OUTLIER) cc_final: 0.7687 (t) REVERT: D 61 GLN cc_start: 0.8999 (pp30) cc_final: 0.8501 (tp-100) REVERT: D 88 VAL cc_start: 0.8660 (OUTLIER) cc_final: 0.8339 (t) REVERT: E 9 MET cc_start: 0.8237 (pmm) cc_final: 0.7679 (ppp) REVERT: E 75 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7307 (pm20) REVERT: E 90 MET cc_start: 0.7853 (mmm) cc_final: 0.7147 (ttm) REVERT: E 91 ARG cc_start: 0.7261 (mtp180) cc_final: 0.6752 (mtm-85) REVERT: K 5 ASN cc_start: 0.8648 (t0) cc_final: 0.8159 (t0) REVERT: K 75 GLN cc_start: 0.8702 (pp30) cc_final: 0.8420 (pp30) REVERT: N 25 GLU cc_start: 0.9363 (mp0) cc_final: 0.9014 (pm20) REVERT: N 58 MET cc_start: 0.5347 (ppp) cc_final: 0.4920 (ppp) REVERT: O 55 ASP cc_start: 0.8454 (p0) cc_final: 0.8094 (p0) REVERT: O 80 LYS cc_start: 0.9436 (tmmt) cc_final: 0.8894 (ptpt) REVERT: P 26 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8026 (tm-30) REVERT: P 39 LYS cc_start: 0.9375 (tttt) cc_final: 0.9073 (tptm) REVERT: P 67 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8558 (mm) REVERT: S 36 TYR cc_start: 0.8913 (OUTLIER) cc_final: 0.8473 (t80) outliers start: 39 outliers final: 32 residues processed: 218 average time/residue: 0.4009 time to fit residues: 136.4796 Evaluate side-chains 221 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 184 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 21 MET Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 27 CYS Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 98 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain P residue 57 ASP Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain S residue 3 ASN Chi-restraints excluded: chain S residue 36 TYR Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 59 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 10.0000 chunk 137 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 149 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 153 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 8 optimal weight: 20.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 GLN O 63 GLN ** P 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.055288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.042201 restraints weight = 191242.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.043440 restraints weight = 82299.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.043548 restraints weight = 38877.061| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 29238 Z= 0.326 Angle : 0.710 14.357 43808 Z= 0.355 Chirality : 0.038 0.306 5606 Planarity : 0.005 0.047 2307 Dihedral : 24.260 173.340 14772 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 22.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 4.69 % Allowed : 29.23 % Favored : 66.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.26), residues: 1029 helix: 0.42 (0.26), residues: 393 sheet: -1.82 (0.36), residues: 181 loop : -1.40 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP P 73 HIS 0.007 0.001 HIS N 45 PHE 0.018 0.002 PHE E 80 TYR 0.019 0.002 TYR N 68 ARG 0.011 0.001 ARG P 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3765.50 seconds wall clock time: 70 minutes 48.73 seconds (4248.73 seconds total)